Add supercell to UEP clustering #78 #79
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Ok. This works fine. We can merge it. |
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However... the PR is connected to issue 61. it has to do with what I did with Eli for beta NMR. The change the mass of the particle. |
Conflicts: pymuonsuite/io/output.py pymuonsuite/muairss.py pymuonsuite/utils.py
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Refactors and adds supercell functionality to
utils.py. The newmake_muonated_supercellis used when clustering in the UEP method. This both accounts for supercell, and sets thecastep_custom_speciesso that if the output format chosen is cell the cell will have the castep symbol for the muon used.Additionally, have refactored a section of
ReadWriteCastep.writeto allowwrite_cellwithout the.paramfile. This is used in the cluster saving, so that the output has the CASTEP settings needed for geometry optimisation (the default task) such as muon mass, gamma, fix_all_atoms ...Closes #78, Closes #61